Transcript: Mouse XM_006501729.3

PREDICTED: Mus musculus SMAD family member 9 (Smad9), transcript variant X2, mRNA.

Source:
NCBI, updated 2016-06-22
Taxon:
Mus musculus (mouse)
Gene:
Smad9 (55994)
Length:
5769
CDS:
343..1608

Additional Resources:

NCBI RefSeq record:
XM_006501729.3
NBCI Gene record:
Smad9 (55994)

sgRNA constructs matching this transcript (CRISPRko, NGG PAM)

This list includes CRISPRko constructs with 100% (20mer + NGG) sequence match to the coding regions of this transcript.

No results found.

shRNA constructs matching this transcript with 100% SDR[?] match

This list includes all shRNAs that have a perfect SDR[?] match to Mouse XM_006501729.3, regardless of what transcript they were originally designed to target. For example, this list can include shRNAs that were originally designed to target: (i) a different isoform or obsolete version of this transcript (as annotated by NCBI), (ii) a transcript of an orthologous gene (in this collection, generally human-to-mouse or mouse-to-human), or (iii) a transcript of a different gene (from the same or different taxon).

Clone ID Target Seq Vector Match Position Match Region[?] SDR Match %[?] Intrinsic Score[?] Adjusted Score[?] Matches Other Mouse Gene?[?] Orig. Target Gene[?] Addgene[?]
1 TRCN0000362883 CGCATCCGAGTCACGTTTATA pLKO_005 1716 3UTR 100% 15.000 21.000 N Smad9 n/a
2 TRCN0000025913 TGTTGCCTACTACGAACTAAA pLKO.1 1029 CDS 100% 13.200 18.480 N Smad9 n/a
3 TRCN0000362814 ATCGTGGCAACCGCAGCTAAT pLKO_005 1659 3UTR 100% 10.800 15.120 N Smad9 n/a
4 TRCN0000362881 TGCATCAACCCATACCATTAC pLKO_005 688 CDS 100% 10.800 7.560 N Smad9 n/a
5 TRCN0000025893 GACTCTTTGGTGAAGAAGTTA pLKO.1 430 CDS 100% 5.625 3.938 N Smad9 n/a
6 TRCN0000025891 ACCAAGACACAGCGAGTACAA pLKO.1 747 CDS 100% 4.950 3.465 N Smad9 n/a
7 TRCN0000025937 CACGGCTTTGAAGTGGTGTAT pLKO.1 1402 CDS 100% 4.950 3.465 N Smad9 n/a
8 TRCN0000025912 GTAAACAGAAACTCGACCATA pLKO.1 1159 CDS 100% 4.950 3.465 N Smad9 n/a
9 TRCN0000090508 GCTGGCCTCAAACTCAGAAAT pLKO.1 4666 3UTR 100% 13.200 6.600 Y Dync1li1 n/a
10 TRCN0000019444 CCCTATCAACACTCAGACTTT pLKO.1 970 CDS 100% 4.950 3.960 N SMAD9 n/a
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shRNA constructs with at least a near match to this transcript

This list includes shRNAs that have at least a >84% (16 of 19 bases) SDR[?] match to the transcript XM_006501729.3, regardless of what transcript they were originally designed to target. For example, this list can include shRNAs that were originally designed to target: (i) a different isoform or obsolete version of this transcript (as annotated by NCBI), (ii) a transcript of an orthologous gene (in this collection, generally human-to-mouse or mouse-to-human), or (iii) a transcript of a different gene (from the same or different taxon). NOTE: this download is a superset of the above result set.

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All ORF constructs matching this transcript

Clone ID DNA Barcode Vector Sequenced %[?] Nuc. Match %[?] Prot. Match %[?] Epitope Tag Match Diffs[?] Addgene[?]
1 ccsbBroadEn_00965 pDONR223 100% 84.6% 94.1% None (many diffs) n/a
2 ccsbBroad304_00965 pLX_304 0% 84.6% 94.1% V5 (many diffs) n/a
3 TRCN0000480230 TCTCGAACATTAGCTTCACAAGTC pLX_317 30.1% 84.6% 94.1% V5 (many diffs) n/a
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